Decoding Protein Dynamics: ProFlex as a Linguistic Bridge in Normal Mode Analysis

Artificial intelligence has revolutionized structural bioinformatics, with AlphaFold being arguably the most impactful development to date. The structural atlases generated by these methods present significant opportunities for unraveling biological mysteries, but also pose challenges in leveraging such massive datasets effectively. In this work, we explore the dynamic landscape of hundreds of thousands of AlphaFold-predicted structures using normal mode analysis. The resulting data is used to define an alphabet summarizing relative protein flexibility, termed ProFlex. We believe that refining and further applying ProFlex-like approaches offers novel opportunities for understanding protein function and enhancing other methods.